Journal Article

Discovery of a minimal form of RNase P in Pyrobaculum

Chan, Patricia P., Cozen, Aaron E., Lowe, Todd M., Bernick, David L., Lai, Lien B., Altman, Sidney, Gopalan, Venkat, Brown, James W.

2010

Overview

RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5' leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes: Nanoarchaeum equitans, Pyrobaculum aerophilum, and Aquifex aeolicus (all hyperthermophiles) [Li Y, Altman S (2004) RNA 10:1533—1540]. A recent study concluded that N. equitans does not have or require RNase P activity because it lacks 5' tRNA leaders. The \"missing\" RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5' pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five Pyrobaculum species and the related crenarchaea Caldivirga maquilingensis and Vulcanisaeta distributa, all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5' tRNA processing activity by high-through-put RNA sequencing and in vitro biochemical assays. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans-acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: active sites / Aquifex / Aquifex aeolicus / Archaeal genomes / Archaeal Proteins - genetics / Archaeal Proteins - isolation & purification / Archaeal Proteins - metabolism / Bacteria / Base Sequence / Biocatalysis / Biochemistry / Biological Sciences / Caldivirga / Caldivirga maquilingensis / Comparative analysis / Computational Biology - methods / Computer applications / Covariance / Electrophoresis, Polyacrylamide Gel / Enzymes / Genes / Genome, Archaeal - genetics / Genomes / Genomics / high-throughput nucleotide sequencing / hyperthermophiles / microorganisms / Molecular Sequence Data / Nanoarchaeum equitans / non-coding RNA / Nucleic Acid Conformation / Nucleotides / prediction / Promoter regions / Pyrobaculum / Pyrobaculum - classification / Pyrobaculum - enzymology / Pyrobaculum - genetics / Pyrobaculum aerophilum / Ribonuclease P / Ribonuclease P - genetics / Ribonuclease P - isolation & purification / Ribonuclease P - metabolism / ribonucleases / Ribonucleic acid / Ribonucleoproteins / Ribozymes / RNA / RNA Precursors - chemistry / RNA Precursors - genetics / RNA Precursors - metabolism / RNA, Archaeal - genetics / RNA, Archaeal - metabolism / RNA, Catalytic - genetics / RNA, Catalytic - metabolism / RNA, Transfer - chemistry / RNA, Transfer - genetics / RNA, Transfer - metabolism / Sequence Homology, Nucleic Acid / Sequencing / Species Specificity / Studies / Substrate Specificity / Transfer RNA / tRNA